I'm not sure, but it seems to me like my wingmen are better programmed to handle default ships than they are to handle custom ships. It's like they automaticaly know the strengths and weeknesses of the default ships, but they don't recognise the strengths and weeknesses of custom ships. They generaly seem to do better in default ships than they do in custom ships, even if the custom ships have the same components as the default ships do. Could it be that the wingmen are programed to recognize the apropriate tactics for the different default ships, but they are not programmed to recognize the apropriate tactics for custom ships based on the actual abilities of the ships?

There are certain ship designs that just work better all the way around. Its kind of an optimum combination based cost of the ship and components provisioned. I've worked for a long time to get my custom ships "optimized". The AI plays much better with my custom ships than with most of the others I've tried.

I always fly my own custom wingmen whenever I can.It's not so much that the AI isn't as good against them, but exchanging shields for more command centres and repairs makes your cheep wingmen last a lot longer in battle.I regularly catch myself with a full fleet of only custom ships.